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1.  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon 
Background
Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes.
Results
Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued.
Conclusions
The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies.
The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/
Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/
doi:10.1186/2041-1480-5-21
PMCID: PMC4089931  PMID: 25009735
Evolutionary biology; Morphological variation; Phenotype; Semantic integration; Bio-ontology
2.  Anatomy ontologies and potential users: bridging the gap 
Journal of Biomedical Semantics  2011;2(Suppl 4):S3.
Motivation
To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations.
Methods
Annotations from three diverse multi-species public-domain datasets provided a set of use cases for matching anatomical terms in two major anatomical ontologies (the Foundational Model of Anatomy and Uberon), using two lexical-matching applications (Zooma and Ontology Mapper).
Results
Approximately 1500 terms were identified; Uberon/Zooma mappings provided 286 matches, compared to the control and Ontology Mapper returned 319 matches. For the Foundational Model of Anatomy, Zooma returned 312 matches, and Ontology Mapper returned 397.
Conclusions
Our results indicate that for our datasets the anatomical entities or concepts are embedded in user-generated complex terms, and while lexical mapping works, anatomy ontologies do not provide the majority of terms users supply when annotating data. Provision of searchable cross-products for compositional terms is a key requirement for using ontologies.
doi:10.1186/2041-1480-2-S4-S3
PMCID: PMC3194170  PMID: 21995944
3.  A Unified Anatomy Ontology of the Vertebrate Skeletal System 
PLoS ONE  2012;7(12):e51070.
The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.
doi:10.1371/journal.pone.0051070
PMCID: PMC3519498  PMID: 23251424
4.  Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature 
PLoS ONE  2010;5(5):e10708.
Background
The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies.
Methodology/Principal Findings
We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators.
Conclusions/Significance
The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.
doi:10.1371/journal.pone.0010708
PMCID: PMC2873956  PMID: 20505755
5.  Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase 
Background
The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying human disease. The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus. The XAO provides consistent terminology that can be applied to anatomical feature descriptions along with a set of relationships that indicate how each anatomical entity is related to others in the embryo, tadpole, or adult frog. The XAO is integral to the functionality of Xenbase (http://www.xenbase.org), the Xenopus model organism database.
Results
We significantly expanded the XAO in the last five years by adding 612 anatomical terms, 2934 relationships between them, 640 synonyms, and 547 ontology cross-references. Each term now has a definition, so database users and curators can be certain they are selecting the correct term when specifying an anatomical entity. With developmental timing information now asserted for every anatomical term, the ontology provides internal checks that ensure high-quality gene expression and phenotype data annotation. The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including images, clones, and publications. Improvements to the XAO structure and anatomical definitions have also enhanced cross-references to anatomy ontologies of other model organisms and humans, providing a bridge between Xenopus data and other vertebrates. The ontology is free and open to all users.
Conclusions
The expanded and improved XAO allows enhanced capture of Xenopus research data and aids mechanisms for performing complex retrieval and analysis of gene expression, phenotypes, and antibodies through text-matching and manual curation. Its comprehensive references to ontologies across taxa help integrate these data for human disease modeling.
doi:10.1186/2041-1480-4-31
PMCID: PMC3816597  PMID: 24139024
Anatomy; Bioinformatics; Data annotation; Developmental biology; Embryology; Model organism database; Ontology; Xenopus
6.  The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age 
Systematic Biology  2010;59(4):369-383.
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.
doi:10.1093/sysbio/syq013
PMCID: PMC2885267  PMID: 20547776
Bioinformatics; devo-evo; fish; morphology; ontology; Teleostei
7.  Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology 
Background
Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species. We developed the Biological Spatial Ontology (BSPO) to standardize the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes.
Results
BSPO currently contains 146 classes and 58 relations representing anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Spatial reasoning is further enhanced in anatomy ontologies by integrating spatial relations such as dorsal_to into class descriptions (e.g., ‘dorsolateral placode’ dorsal_to some ‘epibranchial placode’).
Conclusions
The BSPO is currently used by projects that require standardized anatomical descriptors for phenotype annotation and ontology integration across a diversity of taxa. Anatomical location classes are also useful for describing phenotypic differences, such as morphological variation in position of structures resulting from evolution within and across species.
doi:10.1186/2041-1480-5-34
PMCID: PMC4137724  PMID: 25140222
Anatomy; Spatial relationships; Position; Axes; Reasoning; BSPO; Ontology; Phenotype
8.  The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses 
Plant and Cell Physiology  2012;54(2):e1.
The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.
doi:10.1093/pcp/pcs163
PMCID: PMC3583023  PMID: 23220694
Bioinformatics; Comparative genomics; Genome annotation; Ontology; Plant anatomy; Terpene synthase
9.  The ontology of biological taxa 
Bioinformatics  2008;24(13):i313-i321.
Motivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa.
Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations.
Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information.
Contact: stschulz@uni-freiburg.de
doi:10.1093/bioinformatics/btn158
PMCID: PMC2718636  PMID: 18586729
10.  The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology 
Background
Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards.
Results
The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/.
Conclusions
By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.
doi:10.1186/2041-1480-5-39
PMCID: PMC4177528  PMID: 25276334
Morphology; Taxonomic identification; Phylogenetics; Evolution
11.  The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs 
This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/.
doi:10.3389/fgene.2012.00018
PMCID: PMC3278863  PMID: 22347883
anatomical hierarchy; cell-type assignations; ontology; tissue classification
12.  Applying the functional abnormality ontology pattern to anatomical functions 
Background
Several biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions.
Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately.
Results
We provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions.
Conclusions
Ontological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities.
Availability
The source code and results of our analysis are available at http://bioonto.de.
doi:10.1186/2041-1480-1-4
PMCID: PMC2895731  PMID: 20618982
13.  CELDA – an ontology for the comprehensive representation of cells in complex systems 
BMC Bioinformatics  2013;14:228.
Background
The need for detailed description and modeling of cells drives the continuous generation of large and diverse datasets. Unfortunately, there exists no systematic and comprehensive way to organize these datasets and their information. CELDA (Cell: Expression, Localization, Development, Anatomy) is a novel ontology for the association of primary experimental data and derived knowledge to various types of cells of organisms.
Results
CELDA is a structure that can help to categorize cell types based on species, anatomical localization, subcellular structures, developmental stages and origin. It targets cells in vitro as well as in vivo. Instead of developing a novel ontology from scratch, we carefully designed CELDA in such a way that existing ontologies were integrated as much as possible, and only minimal extensions were performed to cover those classes and areas not present in any existing model. Currently, ten existing ontologies and models are linked to CELDA through the top-level ontology BioTop. Together with 15.439 newly created classes, CELDA contains more than 196.000 classes and 233.670 relationship axioms. CELDA is primarily used as a representational framework for modeling, analyzing and comparing cells within and across species in CellFinder, a web based data repository on cells (http://cellfinder.org).
Conclusions
CELDA can semantically link diverse types of information about cell types. It has been integrated within the research platform CellFinder, where it exemplarily relates cell types from liver and kidney during development on the one hand and anatomical locations in humans on the other, integrating information on all spatial and temporal stages. CELDA is available from the CellFinder website: http://cellfinder.org/about/ontology.
doi:10.1186/1471-2105-14-228
PMCID: PMC3722091  PMID: 23865855
14.  EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update 
Background
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP atlas and is used for annotating gene expression data by the mouse Gene Expression Database (GXD), Edinburgh Mouse Atlas of Gene Expression (EMAGE) and other database resources.
Findings
The original EMAP ontology listed anatomical entities for each developmental stage separately, presented as uniparental graphs organized as a strict partonomy. An "abstract" (i.e. non-stage-specific) representation of mouse developmental anatomy has since been developed. In this version (EMAPA) all instances for a given anatomical entity are presented as a single term, together with the first and last stage at which it is considered to be present. Timed-component anatomies are now derived using staging information in the "primary" non-timed version. Anatomical entities are presented as a directed acyclic graph enabling multiple parental relationships. Subsumption classification as well as partonomic and other types of relationships can now be represented. Most concept names are unique, with compound names constructed using standardized nomenclature conventions, and alternative names associated as synonyms.
Conclusions
The ontology has been extended and refined in a collaborative effort between EMAP and GXD, with additional input from others. Efforts are also underway to improve the revision process with regards to updating and editorial control. The revised EMAPA ontology is freely available from the OBO Foundry resource, with descriptive information and other documentation presented in associated Wiki pages (http://www.obofoundry.org/wiki/index.php/EMAPA:Main_Page).
doi:10.1186/2041-1480-4-15
PMCID: PMC3851555  PMID: 23972281
Mouse development; Anatomy ontology; Developmental anatomy; OBO format
15.  500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton 
Summary
The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2,500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery.
doi:10.1111/j.1439-0426.2012.01985.x
PMCID: PMC3377363  PMID: 22736877
16.  The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio 
Background
The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Danio rerio, from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets.
Results
The ZFA models anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development.
Conclusions
The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease.
doi:10.1186/2041-1480-5-12
PMCID: PMC3944782  PMID: 24568621
17.  A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia 
Systematic Biology  2013;62(5):639-659.
Taxonomic descriptions are unparalleled sources of knowledge of life's phenotypic diversity. As natural language prose, these data sets are largely refractory to computation and integration with other sources of phenotypic data. By formalizing taxonomic descriptions using ontology-based semantic representation, we aim to increase the reusability and computability of taxonomists' primary data. Here, we present a revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New Caledonia using this new model for species description. Descriptive matrices, specimen data, and taxonomic nomenclature are gathered in a unified Web-based application, mx, then exported as both traditional taxonomic treatments and semantic statements using the OWL Web Ontology Language. Character:character-state combinations are then annotated following the entity–quality phenotype model, originally developed to represent mutant model organism phenotype data; concepts of anatomy are drawn from the Hymenoptera Anatomy Ontology and linked to phenotype descriptors from the Phenotypic Quality Ontology. The resulting set of semantic statements is provided in Resource Description Framework format. Applying the model to real data, that is, specimens, taxonomic names, diagnoses, descriptions, and redescriptions, provides us with a foundation to discuss limitations and potential benefits such as automated data integration and reasoner-driven queries. Four species of ensign wasp are now known to occur in New Caledonia: Szepligetella levipetiolata, Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster. A fifth species, Szepligetella sericea, including Szepligetella impressa, syn. nov., has not yet been collected in New Caledonia but can be found on islands throughout the Pacific and so is included in the diagnostic key. [Biodiversity informatics; Evaniidae; New Caledonia; new species; ontology; semantic phenotypes; semantic species description; taxonomy.]
doi:10.1093/sysbio/syt028
PMCID: PMC3739881  PMID: 23652347
18.  Motivation and Organizational Principles for Anatomical Knowledge Representation 
Abstract Objective: Conceptualization of the physical objects and spaces that constitute the human body at the macroscopic level of organization, specified as a machine-parseable ontology that, in its human-readable form, is comprehensible to both expert and novice users of anatomical information.
Design: Conceived as an anatomical enhancement of the UMLS Semantic Network and Metathesaurus, the anatomical ontology was formulated by specifying defining attributes and differentia for classes and subclasses of physical anatomical entities based on their partitive and spatial relationships. The validity of the classification was assessed by instantiating the ontology for the thorax. Several transitive relationships were used for symbolically modeling aspects of the physical organization of the thorax.
Results: By declaring Organ as the macroscopic organizational unit of the body, and defining the entities that constitute organs and higher level entities constituted by organs, all anatomical entities could be assigned to one of three top level classes (Anatomical structure, Anatomical spatial entity and Body substance). The ontology accommodates both the systemic and regional (topographical) views of anatomy, as well as diverse clinical naming conventions of anatomical entities.
Conclusions: The ontology formulated for the thorax is extendible to microscopic and cellular levels, as well as to other body parts, in that its classes subsume essentially all anatomical entities that constitute the body. Explicit definitions of these entities and their relationships provide the first requirement for standards in anatomical concept representation. Conceived from an anatomical viewpoint, the ontology can be generalized and mapped to other biomedical domains and problem solving tasks that require anatomical knowledge.
PMCID: PMC61273  PMID: 9452983
19.  A knowledge based approach to matching human neurodegenerative disease and animal models 
Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species.
doi:10.3389/fninf.2013.00007
PMCID: PMC3653101  PMID: 23717278
phenotype; ontology; Neuroscience Information Framework; neurodegenerative disease; semantics
20.  Experience in Aligning Anatomical Ontologies 
An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts group-to-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.
PMCID: PMC2575410  PMID: 18974854
Ontology; ontology alignment; knowledge representation; anatomy; Semantic Web
21.  The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes 
Nucleic Acids Research  2007;36(Database issue):D768-D772.
The Zebrafish Information Network (ZFIN, http://zfin.org), the model organism database for zebrafish, provides the central location for curated zebrafish genetic, genomic and developmental data. Extensive data integration of mutant phenotypes, genes, expression patterns, sequences, genetic markers, morpholinos, map positions, publications and community resources facilitates the use of the zebrafish as a model for studying gene function, development, behavior and disease. Access to ZFIN data is provided via web-based query forms and through bulk data files. ZFIN is the definitive source for zebrafish gene and allele nomenclature, the zebrafish anatomical ontology (AO) and for zebrafish gene ontology (GO) annotations. ZFIN plays an active role in the development of cross-species ontologies such as the phenotypic quality ontology (PATO) and the gene ontology (GO). Recent enhancements to ZFIN include (i) a new home page and navigation bar, (ii) expanded support for genotypes and phenotypes, (iii) comprehensive phenotype annotations based on anatomical, phenotypic quality and gene ontologies, (iv) a BLAST server tightly integrated with the ZFIN database via ZFIN-specific datasets, (v) a global site search and (vi) help with hands-on resources.
doi:10.1093/nar/gkm956
PMCID: PMC2238839  PMID: 17991680
22.  The mouse pathology ontology, MPATH; structure and applications 
Background
The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated into data collection platforms (such as computerized medical record-keeping systems) to enable the pathologist to rapidly screen and accurately record observations. The MPATH ontology was originally constructed in 2,000 by a committee of pathologists for the annotation of rodent histopathology images, but is now widely used for coding and analysis of disease and phenotype data for rodents, humans and zebrafish.
Construction and content
MPATH is divided into two main branches describing pathological processes and structures based on traditional histopathological principles. It does not aim to include definitive diagnoses, which would generally be regarded as disease concepts. It contains 888 core pathology terms in an almost exclusively is_a hierarchy nine layers deep. Currently, 86% of the terms have textual definitions and contain relationships as well as logical axioms to other ontologies such the Gene Ontology.
Application and utility
MPATH was originally devised for the annotation of histopathological images from mice but is now being used much more widely in the recording of diagnostic and phenotypic data from both mice and humans, and in the construction of logical definitions for phenotype and disease ontologies. We discuss the use of MPATH to generate cross-products with qualifiers derived from a subset of the Phenotype and Trait Ontology (PATO) and its application to large-scale high-throughput phenotyping studies. MPATH provides a largely species-agnostic ontology for the descriptions of anatomic pathology, which can be applied to most amniotes and is now finding extensive use in species other than mice. It enables investigators to interrogate large datasets at a variety of depths, use semantic analysis to identify the relations between diseases in different species and integrate pathology data with other data types, such as pharmacogenomics.
doi:10.1186/2041-1480-4-18
PMCID: PMC3851164  PMID: 24033988
Pathology; Ontology; Disease; Mouse; Phenotype
23.  Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation 
PLoS Biology  2009;7(11):e1000247.
A novel method for quantifying the similarity between phenotypes by the use of ontologies can be used to search for candidate genes, pathway members, and human disease models on the basis of phenotypes alone.
Scientists and clinicians who study genetic alterations and disease have traditionally described phenotypes in natural language. The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally tractable method to mine data resources for mutant phenotypes. In this study, we tested the hypothesis that ontological annotation of disease phenotypes will facilitate the discovery of new genotype-phenotype relationships within and across species. To describe phenotypes using ontologies, we used an Entity-Quality (EQ) methodology, wherein the affected entity (E) and how it is affected (Q) are recorded using terms from a variety of ontologies. Using this EQ method, we annotated the phenotypes of 11 gene-linked human diseases described in Online Mendelian Inheritance in Man (OMIM). These human annotations were loaded into our Ontology-Based Database (OBD) along with other ontology-based phenotype descriptions of mutants from various model organism databases. Phenotypes recorded with this EQ method can be computationally compared based on the hierarchy of terms in the ontologies and the frequency of annotation. We utilized four similarity metrics to compare phenotypes and developed an ontology of homologous and analogous anatomical structures to compare phenotypes between species. Using these tools, we demonstrate that we can identify, through the similarity of the recorded phenotypes, other alleles of the same gene, other members of a signaling pathway, and orthologous genes and pathway members across species. We conclude that EQ-based annotation of phenotypes, in conjunction with a cross-species ontology, and a variety of similarity metrics can identify biologically meaningful similarities between genes by comparing phenotypes alone. This annotation and search method provides a novel and efficient means to identify gene candidates and animal models of human disease, which may shorten the lengthy path to identification and understanding of the genetic basis of human disease.
Author Summary
Model organisms such as fruit flies, mice, and zebrafish are useful for investigating gene function because they are easy to grow, dissect, and genetically manipulate in the laboratory. By examining mutations in these organisms, one can identify candidate genes that cause disease in humans, and develop models to better understand human disease and gene function. A fundamental roadblock for analysis is, however, the lack of a computational method for describing and comparing phenotypes of mutant animals and of human diseases when the genetic basis is unknown. We describe here a novel method using ontologies to record and quantify the similarity between phenotypes. We tested our method by using the annotated mutant phenotype of one member of the Hedgehog signaling pathway in zebrafish to identify other pathway members with similar recorded phenotypes. We also compared human disease phenotypes to those produced by mutation in model organisms, and show that orthologous and biologically relevant genes can be identified by this method. Given that the genetic basis of human disease is often unknown, this method provides a means for identifying candidate genes, pathway members, and disease models by computationally identifying similar phenotypes within and across species.
doi:10.1371/journal.pbio.1000247
PMCID: PMC2774506  PMID: 19956802
24.  Benchmarking Ontologies: Bigger or Better? 
PLoS Computational Biology  2011;7(1):e1001055.
A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.
Author Summary
An ontology represents the concepts and their interrelation within a knowledge domain. Several ontologies have been developed in biomedicine, which provide standardized vocabularies to describe diseases, genes and gene products, physiological phenotypes, anatomical structures, and many other phenomena. Scientists use them to encode the results of complex experiments and observations and to perform integrative analysis to discover new knowledge. A remaining challenge in ontology development is how to evaluate an ontology's representation of knowledge within its scientific domain. Building on classic measures from information retrieval, we introduce a family of metrics including breadth and depth that capture the conceptual coverage and parsimony of an ontology. We test these measures using (1) four commonly used medical ontologies in relation to a corpus of medical documents and (2) seven popular English thesauri (ontologies of synonyms) with respect to text from medicine, news, and novels. Results demonstrate that both medical ontologies and English thesauri have a small overlap in concepts and relations. Our methods suggest efforts to tighten the fit between ontologies and biomedical knowledge.
doi:10.1371/journal.pcbi.1001055
PMCID: PMC3020923  PMID: 21249231
25.  Neuroanatomical domain of the foundational model of anatomy ontology 
Background
The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are expected and valid, no widely adopted approach exists to harmonize different brain labeling protocols and terminologies. Our approach uses the natural organizing framework provided by anatomical structure to correlate terminologies commonly used in neuroimaging.
Description
The Foundational Model of Anatomy (FMA) Ontology provides a semantic framework for representing the anatomical entities and relationships that constitute the phenotypic organization of the human body. In this paper we describe recent enhancements to the neuroanatomical content of the FMA that models cytoarchitectural and morphological regions of the cerebral cortex, as well as white matter structure and connectivity. This modeling effort is driven by the need to correlate and reconcile the terms used in neuroanatomical labeling protocols. By providing an ontological framework that harmonizes multiple views of neuroanatomical organization, the FMA provides developers with reusable and computable knowledge for a range of biomedical applications.
Conclusions
A requirement for facilitating the integration of basic and clinical neuroscience data from diverse sources is a well-structured ontology that can incorporate, organize, and associate neuroanatomical data. We applied the ontological framework of the FMA to align the vocabularies used by several human brain atlases, and to encode emerging knowledge about structural connectivity in the brain. We highlighted several use cases of these extensions, including ontology reuse, neuroimaging data annotation, and organizing 3D brain models.
doi:10.1186/2041-1480-5-1
PMCID: PMC3944952  PMID: 24398054
Data integration; Neuroanatomy; Neuroscience; Ontology; Brain atlas; Neuroinformatics; Information retrieval; mri

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